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Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli

ABSTRACT: Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli

PROVIDER: PRJNA407728 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6048170_1.fastq.gz	Fastqsanger.gz
	SRR6048170_2.fastq.gz	Fastqsanger.gz
	SRR6048180_1.fastq.gz	Fastqsanger.gz
	SRR6048180_2.fastq.gz	Fastqsanger.gz
	SRR6048171_1.fastq.gz	Fastqsanger.gz

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Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli

Project description:Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viablity even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.

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Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli.

Project description:Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.

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Project description:We have successfully characterized R-loop structures using non-denaturing bisulfite treatment coupled with single-molecule sequencing to reveal that R-loops form defined overlapping molecular clusters around promoter, gene body, and terminal regions of genes. Our results uncovers that R-loop formation is both driven by favorable DNA sequence as well as topological state.

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